I certainly sounds like a name matching issue... if it doesn't match exactly, the system may kick out the FF number.
How are you purchasing the tickets? If you always use a TA maybe it's a name entry issue?
The only experience I have that's remotely similar is that when I book tickets for my wife and myself on AA.com (we're both AA PLT/OW SPH), the site won't accept my wife's AA no., even though I'm using her exact same name.
So it's possible, but the online booking engine and direct GDS access are separate systems.
Whatever is happening, my guess is that the name entry is not exactly the same, first/middle/last